There are times where a comparison of signatures is part of our analysis to determine if two people are the same person.
When such an analysis is a part of your research, make certain that what you think is the ancestor's signature is actually his signature. Is the signature you are looking at a transcription of part of a deed in a record book? Record copies at the courthouse in records before some type of image duplication was used are probably the clerk's rendering of the signature.
Two signatures you have for your ancestor may be an actual signature and the other may be a transcription.